Science Research Weekly

Get ready for bone loss mitigation in space mice, a northern paleo-ocean on Mars, a new deep-sea virus, graphs within graphs in SAS, types of statistical contrasts, and a pediatrics grant from the March of Dimes. Science On. References: Bisphosphonate conjugation enhances the bone-specificity of NELL-1-based systemic therapy for spaceflight-induced bone loss in mice Longitudinal genomic surveillance of carriage and transmission of Clostridioides difficile in an intensive care unit Gravity aspects for Mars Identification and genomic analysis of temperate Halomonas bacteriophage vB_HmeY_H4907 from the surface sediment of the Mariana Trench at a depth of 8,900 m Use PROC SGPLOT to embed a graph inside another graph six common types of statistical contrasts An Educational Stroll With Stan – Part 1 Histograms with Two or More Variables in R MD: Pediatric Scientist Development Program R Packages: LearnSL: Learn Supervised Classification Methods Through Examples and Code clustlearn: Learn Clustering Techniques Through Examples and Code

Get ready for Martian mudstone biosignatures, a wide-ranging dwarf planet candidate, mapping mammoth microbes, ice gliding diatoms, extrachromosomal Inocles of the oral microbiome, DNA sequence alignment from scratch in R, and an invitation to check out Science Spotlight. Science On.References:Redox-driven mineral and organic associations in Jezero Crater, MarsDiscovery of a dwarf planet candidate in an extremely wide orbit: 2017 OF201Ancient host-associated microbes obtained from mammoth remainsIce gliding diatoms establish record-low temperature limits for motility in a eukaryotic cellGiant extrachromosomal element “Inocle” potentially expands the adaptive capacity of the human oral microbiomeCreating and managing Canvas quizzes with R/exams and vvcanvasBuilding DNA Sequence Alignment With Needleman-Wunsch Algorithm From Scratch - A Note To My SelfScience SpotlightR Packages:factorH: Multifactor Nonparametric Rank-Based ANOVA with Post Hoc Testsivolcano: Interactive Volcano PlotREXoplanets: Creates Interface with NASA 'Exoplanets Archive API'pmsesampling: Sample Size Determination for Accurate Predictive Linear Regressionminipdf: PDF Document Creatorpower4mome: Power Analysis for Moderation and Mediation

Get ready the Dinosaur Coliseum, cancer-detecting bioengineer bacteria, embedding Unicode into SAS, a web-crawling Katana, and a Million Dollar Bike ride for rare disease research. Science On. References: Clinical efficacy of ONC201 in H3K27M-mutant diffuse midline gliomas is driven by disruption of integrated metabolic and epigenetic pathways Vertebrate ichnology and palaeoenvironmental associations of Alaska’s largest known dinosaur tracksite in the Cretaceous Cantwell Formation (Maastrichtian) of Denali National Park and Preserve Engineered bacteria detect tumor DNA Sustained wet–dry cycling on early Mars Add Unicode symbols and format text labels in SAS Plot confidence intervals for a regression model in SAS Bootstrap confidence intervals for the predicted mean in a regression model Mastering Data Visualization: A Guide to Harnessing the Power of R’s par() Function GitHub: katana NIH/NIA: R43/R44 REDI Award NIH/NIA: R41/R42 REDI Award NSF: Physics Investigator-Initiated Research Projects NSF: Smart Health and Biomedical Research in the Era of Artificial Intelligence and Advanced Data Science Air Force: Science and Technology Fellowship Marfan Foundation: Innovators Grants Million Dollar Bike Ride Pilot Grant Program AAI Intersect Fellowship Program AHA: AIREA McKnight: Scholar Award R-packages: graposas: Graphical Approach Optimal Sample Size osmclass: Classify Open Street Map Features bulkreadr: The Ultimate Tool for Reading Data in Bulk handcodeR: Text Annotation App unicol: The Colors of your University

Get ready for extinct avian genomes, stellar smashing, chemical needles in the haystack, the last Top 40 New CRAN Packages, and career awards at the scientific interface. Science On. References: Genomes of the extinct Bachman’s warbler show high divergence and no evidence of admixture with other extant Vermivora warblers A long-duration gamma-ray burst of dynamical origin from the nucleus of an ancient galaxy BioAutoMATED: An end-to-end automated machine learning tool for explanation and design of biological sequences Therapeutic efficacy of 211At-radiolabeled 2,6-diisopropylphenyl azide in mouse models of human lung cancer A Dual-Gated Structures for Lossless Ion Manipulations-Ion Mobility Orbitrap Mass Spectrometry Platform for Combined Ultra-High-Resolution Molecular Analysis Newsletter June 2023 - Julia 2023 User & Developer Survey - Closing Soon! two types of effect size statistic: standardized and unstandardized May 2023: “Top 40” New CRAN Packages ggplotting power curves from simr package GitHub: Svelte NOSI: Advancing Biomedical Research in Pulmonary Non-Tuberculous Mycobacterial Infections NOSI: Using Targeted Degradation of Protein and non-Protein Targets for the Development of Novel Anti-Infectives North Carolina Biotechnology Center Translational Research Grant American Roentgen Ray Society Scholarship BWF Career Awards at the Scientific Interface R Packages: New CRAN packages that deserve to bask in the light of a new day: flashlighttext: Flashlight Text R Interface GRCRegression: Modified Poisson Regression of Grouped and Right-Censored Counts otargen: Access Open Target Genetics tree3d: 3D Tree Models

Welcome to the final episode of Science Research weekly for 2025. Covering November and December.

Get ready for the PRIMA system to treat age-related blindness, surprising chemistry on Saturn's moon Titan, Kagome tubes for vibration damping in engineering, the R-Multiverse, and a grant on the Foundations of a Resilient Microbiome. Science On.References:Subretinal Photovoltaic Implant to Restore Vision in Geographic Atrophy Due to AMDSnOx Nanoflakes as Enhanced Near-Infrared Photothermal Therapy Agents Synthesized from Electrochemically Oxidized SnS2 PowdersHydrogen cyanide and hydrocarbons mix on TitanTopological polarization of kagome tubes and applications toward vibration isolationPotassium-40 isotopic evidence for an extant pre-giant-impact component of Earth’s mantleOverlay multiple custom density curves on a histogram in SASGo for Launch! Packages Shipped to the R-MultiverseWhat’s new for Python in 2025?leap: Foundations of a Resilient MicrobiomeChan Zuckerberg Initiative: Implementation of Synthetic Biology Principles in ImmunologyR Packages:alpmixBayes: Bayesian Estimation for Alpha-Mixture Survival ModelsbayesQRsurvey: Bayesian Quantile Regression Models for Complex Survey Data Analysisarete: Automated REtrieval from TExtnbpInference: Inference on Average Treatment Effects for Continuous Treatmentspartialling.out: Residuals from Partial Regressions

Get ready for neuronal nanotubes, comet versus alien for interstellar object 3I/ATLAS, rain on the Sun, the R Journal 17/2, citation metric distortion, and more new Science Spotlight videos. Science On.References:Intercellular communication in the brain through a dendritic nanotubular networkIs the Interstellar Object 3I/ATLAS Alien Technology?Spatiotemporal Low First Ionization Potential Abundance: A Catalyst for Coronal CondensationTree swallows as indicators of per- and polyfluoroalkyl substance exposure and effects at select Department of Defense sites along the East Coast and at sites with different sources in the Upper Midwest, United States90% of science is lost. This new AI just found itR Journal Volume 17/2New, work-in-progress book on spatial data visualization in RBeyond Fraud: How IHME Distorts Academic MetricsScience SpotlightR Packages:descsuppRplots: Generate Plots for All Variables in Descriptive Tablesmedicalcoder: Tools for Working with ICD Codes and Comorbidity AlgorithmsGINAX: Performs Genome-Wide Iterative Fine-Mapping for Non-Gaussian Data using GINA-XeasyRef: Easy Reference Generation for R Packages

Get ready for chromosomal instability suppression in breast cancer, the marine origins of leeches, metal-laced hydrogels, better simulations in R, and a grant on Precision Mitochondria. Science On.References:Epigenetic regulation of chromosomal instability by EZH2 methyltransferaseThe first leech body fossil predates estimated hirudinidan origins by 200 million yearsHydrogel-Based Vat Photopolymerization of Ceramics and Metals with Low Shrinkages via Repeated Infusion PrecipitationDeploy Multiple Shiny Apps from One R PackageA new simstudy function to make simulating replications easierARIA: Precision MitochondriaR Packages:mda.biber: Functions for Multi-Dimensional Analysispwranova: Power Analysis of Flexible ANOVA Designs and Related Testssummarytabl: Generate Summary Tables for Continuous, Ordinal, and Categorical Data

Get ready for direct pain relief, pollutant breakdown with biochar, shark-attack resistant wetsuits, an updated timetree for Fungi, edible electronics, simulating the Monty Hall problem in R, the Top 40 New CRAN Packages for August 2025, and the DARPA Young Faculty Award. This episode covers material from September 26th to October 2nd. Science On.References:Targeting prostaglandin E2 receptor 2 in Schwann cells inhibits inflammatory pain but not inflammationThe geologic history of marine dissolved organic carbon from iron oxidesStructure-performance relationship of biochar for direct degradation of organic pollutantsDOLPHIN advances single-cell transcriptomics beyond gene level by leveraging exon and junction readsEffectiveness of bite-resistant materials to reduce injuries from white shark (Carcharodon carcharias) and tiger shark (Galeocerdo cuvier) bitesNanotechnology-driven coordination of shoot–root systems enhances rice nitrogen use efficiencyDetection of organic compounds in freshly ejected ice grains from Enceladus’s oceanA timetree of Fungi dated with fossils and horizontal gene transfersPrinted Integrated Logic Circuits Based on Chitosan-Gated Organic Transistors for Future Edible SystemsSimulating Monty Hall’s ProblemPlotting Distributions in RAugust 2025 Top 40 New CRAN PackagesSpurious Correlations in R – Correlation is not CausationLearning And Exploring The Workflow of RNA-Seq Analysis – A Note To MyselfDARPA: Young Faculty Award (YFA) 2026R Packages:eDNAfuns: Working with Metabarcoding Data in a Tidy Formatspuriouscorrelations: Datasets with Strong and Spurious Correlations

Get ready for a review of acetaminophen and neurodevelopmental disorders, dehydration and stress response, Hycean world woes, hints at the compositional protein code, fraudulent publishing in mathematics, R Journal Volume 17/1, and a grant on microbial dust control for mining operations. Science On.References:Evaluation of the evidence on acetaminophen use and neurodevelopmental disorders using the Navigation Guide methodologyHabitual fluid intake and hydration status influence cortisol reactivity to acute psychosocial stressSub-Neptunes Are Drier than They Seem: Rethinking the Origins of Water-rich WorldsA domed pachycephalosaur from the early Cretaceous of MongoliaTracing the Origin of the Genetic Code and Thermostability to Dipeptide Sequences in ProteomesTiny protein pairs may hold the secret to life’s originHow to Fight Fraudulent Publishing in the Mathematical Sciences: Joint Recommendations of the IMU and the ICIAMFraudulent Publishing in the Mathematical SciencesThe R Journal Volume 17/1Birthdays and the coupon collector's problemNIH: Pilot Projects to Enhance the Human Virome ProgramNIH: Clinical Trial Readiness for Rare Diseases, Disorders, and SyndromesNSF/CASIS Transport Phenomena Research at the International Space Station to Benefit Life on EarthMicrobial dust control and surface stabilizationR Packages:bnpMTP: Bayesian Nonparametric Sensitivity Analysis of Multiple Testing Procedures for p ValuesMicrobTiSDA: Microbiome Time-Series Data Analysisplumber2: Easy and Powerful Web ServersggDNAvis: 'ggplot2'-Based Tools for Visualising DNA Sequences and Modifications

Get ready for maize shoot stem cells, a five image Einstein cross, identity of some Little Red Dots, ATREIDES for exo-Neptunes, Volume 114 of the Journal of Statistical Software, ggplot2 geoms and stats, and Classic Scientific Paper Review. Science On.References:Journal of Statistical Software Volume 114Large-scale single-cell profiling of stem cells identifies redundant regulators of shoot development and yield trait variationHerS-3: An Exceptional Einstein Cross Reveals a Massive Dark Matter HaloA remarkable ruby: Absorption in dense gas, rather than evolved stars, drives the extreme Balmer break of a little red dot at z = 3.5Journal of Statistical Software Volume 114All the Ways to Programmatically Edit or Parse R Markdown / Quarto DocumentsLearning About Assemblying DNA, BLAST, and Multiple Loci Sequence Testing (MLST) – A Note To MyselfExploring {ggplot2}’s Geoms and StatsClassic Scientific Paper ReviewR Packages:henna: A Versatile Visualization Suiteccar3: Canonical Correlation Analysis via Reduced Rank RegressionSurvGME: Analysis of Survival Data under Graphical and Measurement Error Modelsworkspace: Manage Collections of Datasets and Objects

Get ready for the failure of beta-blockers, cathartocytosis, flagging suspicious journals with AS, extreme ankylosaur armor, the basics of phylogenetic analysis in R, and a tiny space grant from DevelopSpace. Science On.References:Human endogenous retrovirus K (HERV-K) envelope structures in pre- and postfusion by cryo-EMBeta-Blockers after Myocardial Infarction without Reduced Ejection FractionCathartocytosis: Jettisoning of cellular material during reprogramming of differentiated cellsEstimating the predictability of questionable open-access journalsExtreme armour in the world’s oldest ankylosaurPatterned invagination prevents mechanical instability during gastrulationLearning The Basics of Phylogenetic AnalysisDevelopSpace grantR Packages:blendR: Blended Survival CurvesCompClassMetrics: Classification Measures when Subclasses are InvolvedTrialSimulator: Clinical Trial SimulatorRnaught: Estimate the Basic Reproduction Number (R0)metamorphr: Tidy and Streamlined Metabolomics Data WorkflowstastyR: Recipe Data from 'Allrecipes.com'

Get ready for deep-ocean oxidation dates, no giant impact for Jupiter’s core, common meds making antibiotic resistance worse, arsenic-mineralizing marine worms, the July 2025 Top 40 new CRAN packages, a plea for PyPAN: the Python Package Archive Network, and a grant on aging mammalian tissues in vitro. Science On. References:Mid-Devonian ocean oxygenation enabled the expansion of animals into deeper-water habitatsNo dilute core produced in simulations of giant impacts on to JupiterThe effect of commonly used non-antibiotic medications on antimicrobial resistance development in Escherichia coliA deep-sea hydrothermal vent worm detoxifies arsenic and sulfur by intracellular biomineralization of orpiment (As2S3)July 2025 Top 40 New CRAN PackagesHow many parameters does GPT-5 have?Python needs its CRANThe European Bioconductor ConferenceNIH: Aging Mammalian Tissues In VitroNIH: Stephen I. Katz Early Stage Investigator Research Project Grant (non-clinical trial)NIH: Stephen I. Katz Early Stage Investigator Research Project Grant (human subjects)R Packages:ham: Healthcare Analysis Methodsmultideploy: Deploy File Changes Across Multiple 'GitHub' RepositoriesSampleSizeCalculator: Sample Size Calculator under Complex Survey Designtidypopgen: Tidy Population Geneticsmlspatial: Machine Learning and Mapping for Spatial Epidemiologygwas2crispr: GWAS-to-CRISPR Data Pipeline for High-Throughput SNP Target Extractionggdiceplot: Dice Plot Visualization for 'ggplot2'

Get ready for a potential cancer vaccine, a carbon ring stabilized by smaller rings, Uranus’ newest tiny moon, absurd conversions in R, and funding from the American Lung Association. Science On.References:Sensitization of tumours to immunotherapy by boosting early type-I interferon responses enables epitope spreadingSolution-phase stabilization of a cyclocarbon by catenane formationSwRI-led Webb Telescope survey discovers new moon orbiting UranusPython Developers Survey 2024 ResultsHandling Missing Data in R: A Comprehensive GuideLearning Antimicrobial Resistance (AMR) genes with BioconductorLittle useless-useful R functions – Absurd converter with Markdown reportAmerican Lung Association: Awards and Grants OpportunitiesR Packages:Nematode: Ecological Indices Calculator for Nematode CommunitiesconfidenceCurves: Frequentist Confidence Analysis for Clinical Trialsggdiagram: Object-Oriented Diagram Plots with 'ggplot2'csdb: An Abstracted System for Easily Working with Databases with Large Datasetsgtregression: Tools for Creating Publication-Ready Regression Tables

Get ready for Antarctic submarine canyons, a medicated gel for diabetic wound healing, rapid electronic detection of infectious and chronic diseases, SAS and R in tandem, and several grants from private foundations. Science On.References:The geomorphometry of Antarctic submarine canyonsEngineered sEVs encapsulated in GelMA facilitated diabetic wound healing by promoting angiogenesis via targeting thrombospondin-1 Nanoparticle-Supported, Rapid, and Electronic Detection of SARS-CoV-2 Antibodies and Antigens at the Subfemtomolar LevelBuilding seamless data pipelines across multiple languages: A life sciences and healthcare use case leveraging R and SASGateway for Cancer Research Grant ProgramIAFNS Cognitive Health Committee Request for ProposalsSimons Collaborations in Ecology and Evolution

Get ready for the power of iNaturalist in biodiversity research, mechanisms behind lightning strikes, multi-region brain organoids, programmable chromosome engineering, an idealized double-slit experiment, why hardware may need a new foundation, animated maps in R, and a grant from PepsiCo on novel proteins. Science On.References:iNaturalist accelerates biodiversity research Photoelectric Effect in Air Explains Lightning Initiation and Terrestrial Gamma Ray FlashesMulti-Region Brain Organoids Integrating Cerebral, Mid-Hindbrain, and Endothelial SystemsIterative recombinase technologies for efficient and precise genome engineering across kilobase to megabase scalesInhibition of the minor spliceosome restricts the growth of a broad spectrum of cancersCoherent and Incoherent Light Scattering by Single-Atom Wave PacketsEinstein was wrong: MIT just settled a 100-year quantum debateSurfactants Steer Supraparticle StructureJournal of Statistical Software Volume 113Why Hardware Needs a New Foundation3 ways to estimate parameters when fitting a distribution to dataIntroduction to Generalised Linear Models with Prussian Horse KicksAnimated Maps with {ggplot2} and {gganimate}Novel proteins, peptides and amino acids with health benefits

Get ready for cancer cells going up in sugary flames, live-action planetary formation, deep sea plastic biodegradation, a 150-year-old museum fossil specimen finally gets figured out, The R Journal: Volume 16/4, dealing with non-values in R, and some Science Spotlights. Science On.References:A Novel Exopolysaccharide, Highly Prevalent in Marine Spongiibacter, Triggers Pyroptosis to Exhibit Potent Anticancer EffectsLiDO: Discovery of a 10:1 Resonator with a Novel Libration StateRefractory solid condensation detected in an embedded protoplanetary diskUnveiling deep-sea biodegradation of microbially produced lactate-based polyester (LAHB) via plastisphere metagenomics and metatranscriptomicsPalaeocampa anthrax, an armored freshwater lobopodian with chemical defenses from the CarboniferousThe R Journal: Volume 16/4Let’s talk about NA-s!What is Biological Dark Matter?What Makes Functional Precision Cancer Therapy Useful?R Packages:dependentsimr: Simulate Omics-Scale Data with DependencyROCnGO: Fast Analysis of ROC Curves

Get ready for Parkinson’s disease sniffing dogs; the bladed microtube scheme for massive magnetic fields; a giant, spinning black hole merger; ghost galaxies; lasagna plots in SAS; and an NSF grant on Programmable Cloud Laboratories. Science On.References:Trained dogs can detect the odor of Parkinson's diseaseGigagauss magnetic field generation by bladed microtube implosionDynamic Organization of Cells in Colonic Epithelium is Encoded by Five Biological RulesGW231123: a Binary Black Hole Merger with Total Mass 190-265 Encoding hierarchical 3D architecture through inverse design of programmable bonds100 ghost galaxies may be orbiting the Milky Way—and we’re just now uncovering themJournal of Statistical Software Volume 113Use a lasagna plot to visualize US gas pricesExploring R and Rust in Bioinformatics – Online Developer Forum, 28 July 2025How to choose an IDEStandard Deviation vs. Standard Error: Meaning, Misuse, and the Math Behind the ConfusionNSF Test Bed: Toward a Network of Programmable Cloud LaboratoriesNASA ROSES 2025: F.9 Citizen Science Seed Funding ProgramR Packages:rfriend: Provides Batch Functions and Visualisation for Basic Statistical ProceduresclusterWebApp: Universal Clustering Analysis PlatformfusedTree: Fused Partitioned Regression for Clinical and Omics Dataironseed: Improved Random Number Generator Seedingjunco: Create Common Tables and Listings Used in Clinical Trialsggtranslate: A 'ggplot2' Extension for Translating Plot Text

Get ready for Big Five Workouts, CryoRhodopsins, double detonation supernovae, moon-rice, the 4 layers of testing for R packages, and a three-track grant from the NSF on Translation to Practice. Science On.References:Personality traits can predict which exercise intensities we enjoy most, and the magnitude of stress reduction experienced following a training programCryoRhodopsins: A comprehensive characterization of a group of microbial rhodopsins from cold environmentsThe genome of a sea spider corroborates a shared Hox cluster motif in arthropods with a reduced posterior tagmaRegulating Multifunctional Oxygen Vacancies for Plasma-Driven Air-to-Ammonia ConversionCalcium in a supernova remnant as a fingerprint of a sub-Chandrasekhar-mass explosionRestoration of striatal neuroprotective pathways by kinase inhibitor treatment of Parkinson’s disease–linked LRRK2-mutant miceMoon-Rice: Developing the perfect crop for space-basesThe 4 Layers of Testing Every R Package NeedsElevate Your Skills and Boost Your Career with Jumping Rivers Free Monthly WebinarsNSF: National Science Foundation Translation to PracticeR Packages:BMIselect: Bayesian MI-LASSO for Variable Selection on Multiply-Imputed Datasetsgggda: A 'ggplot2' Extension for Geometric Data Analysisreptiledbr: Interface to the Reptile Database for Querying and Retrieving Taxonomic DatasemEffect: Structural Equation Model Effect Analysis and Visualization

Get ready for cancer cell states, ADHD diagnosis difficulties, body profiles from Ediacaran trace fossils, LMMS for work you can do yourself, May 2025 Top 40 New CRAN Packages, and a Google Research grant for Quantum Neuroscience. This episode covers materials from June 27th to July 3rd. Science On.References:AAnet resolves a continuum of spatially-localized cell states to unveil intratumoral heterogeneityDiagnosing ADHD in adults in randomized controlled studies: a scoping reviewQuantitative decoding of Ediacaran locomotory trace fossil morphologies: Evidence for the emergence of slender anterior-posterior body profiles Size-Insensitive Vapor Diffusion Enabled by Additive Freeze-Printed Aerogels for Scalable DesalinationYou can outsource the grunt work to an LLM, not expertiseMay 2025 Top 40 New CRAN PackagesBeyond the Basics: Books to Supercharge Your R SkillsDOD: Air Force Fiscal Year 2026 Young Investigator Program (YIP)NASA: Innovative Advanced Concepts (NIAC) Phase IGoogle Research: Quantum NeuroscienceR Packages:autograph: Automatic Plotting of Many GraphsgemR: General Effect Modelling